For 2009 (the year of incorporation) our S Corp used only 2 independent contractors, paid them via check, and incurred a few expenses. The contractors were issued 1099's for their compensation. The S Corp never filed form 941 quarterly. Is an S corp with only 1099 contractors still required to file form 941 quarterly and form 940 annually?

Generally speaking, you are not required to file a 941 quarterly report provided you have informed the IRS earlier that you do not intend to hire any employees. If the IRS is not aware of this or that in the past you had an employee on the payroll and you had filed prior 941 quarterly tax returns, then the IRS will certainly send you notices in the mail requesting the filing of these 941 tax returns.

Thus, the answer to your question is that your S Corporation generally is not required to file the 941 or 940 tax returns, but, it is best to file them if the IRS has requested a 941 and you should indicate a "Zero" Wages and submit it the IRS.